Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate NP_349006.1 CA_C2391 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase
Query= SwissProt::Q9Z4S1 (397 letters) >NCBI__GCF_000008765.1:NP_349006.1 Length = 408 Score = 374 bits (960), Expect = e-108 Identities = 204/393 (51%), Positives = 263/393 (66%), Gaps = 4/393 (1%) Query: 7 FSYAGVHCRIKRKRK-DLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGIRAI 65 F GV IK K DL +I+SE PC AAG FTTN VKAAPV+ D++ + I AI Sbjct: 18 FKAIGVASGIKGNNKSDLCVIYSEKPCIAAGTFTTNKVKAAPVLLDLKHI--ESENIYAI 75 Query: 66 TVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESGIEE 125 NSG ANACTG+ G A MAE TAK L I E VLV+STGVIGV LP++KV GIE+ Sbjct: 76 VANSGNANACTGDDGYEKAYLMAECTAKHLKIKPEEVLVASTGVIGVPLPIDKVMFGIEK 135 Query: 126 AVKNLSKDPVPFA-EAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATMLSF 184 A L K A +AIMTTDT K + ++ K++T+ IAKGSGMIHPNMATMLSF Sbjct: 136 AFSILPKSDANKAIDAIMTTDTVQKKIFVEFMLDKKKVTICAIAKGSGMIHPNMATMLSF 195 Query: 185 ITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETDGFW 244 I TDAN+++D L K LK SV DSYNMI VD DTSTNDM ++LANG +GN I E + Sbjct: 196 IVTDANITKDLLNKALKESVKDSYNMISVDRDTSTNDMALLLANGASGNTLISSENSDYE 255 Query: 245 KLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKTAIYG 304 +A+H VN +++ I +DGEGATK+IE +V A A++ A+++++SNLVK A++G Sbjct: 256 VFKKALHYVNVEISKMIAKDGEGATKLIEAKVFGASSSRDAKVAAKSVITSNLVKAAVFG 315 Query: 305 EDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDTAKKILSEKKV 364 DANWGR+I A GYS A+ DP ++D+ F + +++ G G++FDE+ AKKIL V Sbjct: 316 SDANWGRIICALGYSAAEIDPSKVDISFSNNDSKVETCLKGTGLNFDEEAAKKILDGDHV 375 Query: 365 KIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 I +++ GK A AWGCDLT YV+ING YR+ Sbjct: 376 IIEVNLNNGKFNATAWGCDLTYDYVKINGSYRS 408 Lambda K H 0.315 0.133 0.371 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 430 Number of extensions: 18 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 397 Length of database: 408 Length adjustment: 31 Effective length of query: 366 Effective length of database: 377 Effective search space: 137982 Effective search space used: 137982 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory